title: The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.
abstract: We developed a pair of databases that support two important tasks: annotation of anonymous RNA transcripts and discovery of novel non-coding RNAs. The database combo is called the Functional RNA Database and consists of two databases: a rewrite of the original version of the Functional RNA Database (fRNAdb) and the latest version of the UCSC GenomeBrowser for Functional RNA. The former is a sequence database equipped with a powerful search function and hosts a large collection of known/predicted non-coding RNA sequences acquired from existing databases as well as novel/predicted sequences reported by researchers of the Functional RNA Project. The latter is a UCSC Genome Browser mirror with large additional custom tracks specifically associated with non-coding elements. It also includes several functional enhancements such as a presentation of a common secondary structure prediction at any given genomic window < or =500 bp. Our GenomeBrowser supports user authentication and user-specific tracks. The current version of the fRNAdb is a complete rewrite of the former version, hosting a larger number of sequences and with a much friendlier interface. The current version of UCSC GenomeBrowser for Functional RNA features a larger number of tracks and richer features than the former version. The databases are available at http://www.ncrna.org/.
authors.affiliation: National Institute of Advanced Industrial Science and Technology, Computational Biology Research Center, Tokyo 135-0064, Japan. mituyama-toutai@aist.go.jp
authors.forename: Toutai
authors.initials: T
authors.lastname: Mituyama
authors.forename: Kouichirou
authors.initials: K
authors.lastname: Yamada
authors.forename: Emi
authors.initials: E
authors.lastname: Hattori
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Okida
authors.forename: Yukiteru
authors.initials: Y
authors.lastname: Ono
authors.forename: Goro
authors.initials: G
authors.lastname: Terai
authors.forename: Aya
authors.initials: A
authors.lastname: Yoshizawa
authors.forename: Takashi
authors.initials: T
authors.lastname: Komori
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D023281:Genomics; D006801:Humans; D051379:Mice; D022661:RNA, Untranslated / Q000737:chemistry* / Q000502:physiology; D051381:Rats; D017423:Sequence Analysis, RNA
chemical_list: D022661:RNA, Untranslated